Interpretive Summary: All plant and animal cells contain organelles called mitochondria that convert food to energy. The mitochondria contain small amount of unique DNA, but much less DNA than chromosomes in the nucleus. In plants, the plastids, another organelle found only in plants, and responsible for capturing sunlight and converting it to energy, also contains small amounts of DNA. The sequence of DNA in mitochondria, chromosomes, and plastids is of interest in helping us understand how cells work and genes are inherited. In this study we developed a technique to readily determine the entire DNA sequence of the mitochondria and of the plastid of carrot cells using the most advanced “next generation” DNA sequencing methods. This is the first tool developed that is able to do this with “next generation” sequencing without extensive preparation of the DNA. Using this technique, we discovered evidence that DNA in the carrot mitochondrion has moved to the carrot plastid. This is the first report of DNA transfer into plastid genomes of higher plants. This study is to biologists, geneticists, plant scientists, and plant breeders.

Technical Abstract:
Sequence analysis of organelle genomes has revealed important aspects of plant cell evolution. The scope of this study was to develop an approach for de novo assembly of the carrot mitochondrial genome using next generation sequence data from total genomic DNA. Sequencing data from a carrot 454 whole genome library were used to develop a de novo assembly of the mitochondrial genome. Development of a new bioinformatic tool allowed visualizing contig connections and elucidation of the de novo assembly. Southern hybridization demonstrated recombination across two large repeats. Genome annotation allowed identification of 44 protein coding genes, three rRNA and 17 tRNA. Intergenic sequence analysis allowed detection of a fragment of DNA specific to the carrot plastid genome. PCR amplification and sequence analysis across different Apiaceae species revealed consistent conservation of this fragment in the mitochondrial genomes and an insertion in Daucus plastid genomes, giving evidence of a mitochondrial to plastid transfer of DNA. Sequence similarity with a retrotransposon element suggests a possibility that a transposon-like event transferred this sequence into the plastid genome. This study confirmed that whole genome sequencing is a practical approach for de novo assembly of higher plant mitochondrial genomes. In addition, a new aspect of intercompartmental genome interaction was reported providing the first evidence for DNA transfer into an angiosperm plastid genome. The approach used here could be used more broadly to sequence and assemble mitochondrial genomes of diverse species. This information will allow us to better understand intercompartmental interactions and cell evolution.